Get expression matrix from Seurat Object

getExpressionMatrix(
  so,
  only.variable = F,
  which.assay = NULL,
  which.data = "scale",
  use.additional.genes = NA,
  as.dense = F
)

Arguments

so

Seurat Object

only.variable

Logical indicating whether to include variable features only or not.

which.assay

Seurat assay to get data from. Default is DefaultAssay(so).

which.data

Specify which data to use (refers to slots in Seurat object assay). One of:

use.additional.genes

Character vector of additional genes to include (in addition to varibale, if variable flag is specificed). Default is NA.

as.dense

Logical to convert sparse to dense matrix. Only applies if which.data is 'data'. Default is FALSE.

gene x cell expression matrix

Nicholas Mikolajewicz